# File name: qqmultinorm.R
# Version: 1.1
# Last updated: 2009-08-28
#
# This R-code is made by:
# Mikkel Meyer Andersen, Denmark
# mikl [funny-a] math [.] aau [.] dk or 
# mikl [funny-a] mikl [.] dk
#
# Licence: GPLv2
#
# Feel free to use it, but if you do I'll like to hear about it (just for fun).
# If you make corrections, please submit them back so others can enjoy them as well.
 
qqchisq <- function(y, main, df=2, continuity.correction = 0.5)
{
  n <- length(y)
  y <- sort(y)
  c <- numeric(n)
 
  for (i in 1:n)
    c[i] <- qchisq((i-continuity.correction)/n, df=df)
 
  plot(c, y, xlab="Theoretical Quantiles", ylab="Sample Quantiles", main=main)
  lines(c(c[1], c[n]), c(c[1], c[n]), type="l")
}
 
dec2bin <- function(x)
{
  if (!is.vector(x) || length(x) != 1 || x < 0)
    stop("x must be a non-negative integer")
 
  N <- length(x)
  ndigits <- floor(log2(x)) + 1
  bin <- numeric(ndigits)
 
  for (i in (ndigits-1):0)
  {
    tmp <- 2^i
 
    if (x %/% tmp >= 1)
    {
      bin[i+1] <- 1
      x <- x - tmp
    }
  }
 
  return(rev(bin))
}
 
# Returns the power set without the empty set
power.set <- function(v)
{
  n <- length(v)  
  N <- 2^n - 1
  ps <- vector("list", N)
 
  for (i in 1:(N-1))
  {
    Nbin <- dec2bin(i)
    Nbin <- c(numeric(n-length(Nbin)), Nbin)
    Nbin <- rev(Nbin)
    ps[[i]] <- v[which(Nbin == 1)]
  }
 
  ps[[N]] <- v
 
  return(ps)
}
 
# Input: n
#  - here the number of plots
# Returns c(h, w)
#  - the optimal choice of rows and cols to use in in mfrow
find.optimal.mfrow.size <- function(n)
{  
  w0 <- ceiling(sqrt(n))
 
  # The area can at max contain of 10% unused space
  max.error <- round(n*0.1)
 
  n.minus.error <- n - max.error
  n.plus.error <- n + max.error
 
  # If n is a square, fine!
  if (w0^2 == n)
    return(c(w0, w0))
 
  # Col 1 and 2: w and h
  # Col 3: The difference between w and h: this should be as small as possible
  candidates <- matrix(ncol=3)
 
  for (w in w0:1)  
  {    
    h <- ceiling(n / w)
    n0 <- w*h
 
    # Because of ceiling we know that n0 >= n
    if (n0 <= n.plus.error)
      candidates <- rbind(candidates, c(h, w, abs(w-h)))
  }
 
  # First row is NA
  candidates <- candidates[-1,]
 
  # Uups, something went wront - well, don't panic
  if (nrow(candidates) == 0)
    return(c(w0, w0))
 
  # First order by abs(w-h) and then by h to get a widescreen-look 
  # instead of a poster-look
  candidates <- candidates[order(candidates[,3], candidates[,1]), ]
 
  return(candidates[1, c(1,2)])
}
 
# dataset: variables in columns and observations as rows
# subset.min.size, subset.max.size: inclusive limits
# filename: if specified, the plot are saved as a png file with this filename
qqmultinorm <- function(dataset, subset.min.size = 1, subset.max.size = 4, filename = NULL, use.optimale.size = F)
{
  p <- ncol(dataset)
  n <- nrow(dataset)
 
  if (subset.min.size < 1) stop("subset.min.size < 1")
  if (subset.min.size > p) stop("subset.min.size > p")
  if (subset.max.size < 1) stop("subset.max.size < 1")
  if (subset.max.size > p) stop("subset.max.size > p")
  if (subset.min.size > subset.max.size) stop("subset.min.size > subset.max.size")
 
  if (is.null(colnames(dataset)))
    colnames(dataset) <- 1:p
 
  # We have p variables. If all is to be checked against each other,
  # then we have a power-set with 2^p subsets (including the empty set)
 
  # Here we get subset containing indexes of the variables to include
  # Note that power.set doesn't include the empty set.
  subsets <- power.set(1:p)
  subsets.len <- length(subsets)
 
  # To get the plots with the fewest variables first, we do a litte trick:
  # While we find out which plots to include, we build a list
  # where each element of a list is the index of the subset,
  # and the index of the element is the size of the subset.
  # (The +1 is because the limits are includesive!)
  s.included <- vector("list", subset.max.size - subset.min.size + 1)
 
  plots <- 0
 
  for (i in 1:subsets.len)
  {
    s <- subsets[[i]]
    s.len <- length(s)
 
    if (s.len >= subset.min.size && s.len <= subset.max.size)
    {
      plots <- plots + 1
      s.included[[s.len - subset.min.size + 1]] <- c(s.included[[s.len - subset.min.size + 1]], i)
    }
  }
 
  # Now it's possible to build the subset index vector; 
  # we disregard the size of each subset; no more need to know it.
  s.indexes <- c()
 
  for (s in s.included)
  {
    s.indexes <- c(s.indexes, s)
  }
 
  # We want the best view  
  plot.per.row <- ceiling(plots^(1/2))
  plot.per.column <- ceiling(plots^(1/2))
 
  if (use.optimale.size)
  {
    mfrow.parameters <- find.optimal.mfrow.size(plots)
    plot.per.row <- mfrow.parameters[1]
    plot.per.column <- mfrow.parameters[2]
  }
 
  plot.width <- 300
  plot.height <- 200
 
  if (!is.null(filename))
    png(file=paste(filename, ".png", sep=""), bg="white", width = plot.per.row * plot.width, height = plot.per.column * plot.height)
 
  par(mfrow = c(plot.per.row, plot.per.column))  
 
  # There's no need to calculate a whole lot several times:
  ybar <- as.vector(colMeans(dataset))
 
  S <- as.matrix(var(dataset))
 
  current <- 1  
  for (i in s.indexes)
  {
    s <- subsets[[i]]
    s.len <- length(s)
 
    if (s.len > subset.max.size)
      next
 
    cat("Processing subset no.", current, "out of", plots, "\n")
 
    # Container for our values
    squared.dist <- numeric(n)
 
    # qr.solve(A) = A^(-1)  
    Sinv <- qr.solve(S[s,s])
 
    # Then calculate the squared distance for each datapoint
    for (i in 1:n)
    {
      c <- dataset[i,s] - ybar[s]
      squared.dist[i] <- t(c) %*% Sinv %*% c
    }
 
    # Finding the order statistic
    squared.dist <- sort(squared.dist)
 
    qqchisq(squared.dist, paste(colnames(dataset)[s], collapse=", "), s.len)
 
    current <- current + 1
  }
 
  if (!is.null(filename))
    dev.off()
}
 
# Example:
A <- matrix(rnorm(2000, mean=3, sd=2), ncol=8)
qqmultinorm(A, 2, 2, "multinorm-optimal.size", use.optimale.size = T)
qqmultinorm(A, 2, 2, "multinorm", use.optimale.size = F)

# File name: qqmultinorm.R
#
# This R-code is made by:
# Mikkel Meyer Andersen, Denmark
# mikl [funny-a] math [.] aau [.] dk or 
# mikl [funny-a] mikl [.] dk
#
# Licence: GPLv2
#
# Feel free to use it, but if you do I'll like to hear about it (just for fun).
# If you make corrections, please submit them back so others can enjoy them as well.
 
qqchisq <- function(y, main, df=2, continuity.correction = 0.5)
{
  n <- length(y)
  y <- sort(y)
  c <- numeric(n)
 
  for (i in 1:n)
    c[i] <- qchisq((i-continuity.correction)/n, df=df)
 
  plot(c, y, xlab="Theoretical Quantiles", ylab="Sample Quantiles", main=main)
  lines(c(c[1], c[n]), c(c[1], c[n]), type="l")
}
 
dec2bin <- function(x)
{
  if (!is.vector(x) || length(x) != 1 || x < 0)
    stop("x must be a non-negative integer")
 
  N <- length(x)
  ndigits <- floor(log2(x)) + 1
  bin <- numeric(ndigits)
 
  for (i in (ndigits-1):0)
  {
    tmp <- 2^i
 
    if (x %/% tmp >= 1)
    {
      bin[i+1] <- 1
      x <- x - tmp
    }
  }
 
  return(rev(bin))
}
 
# Returns the power set without the empty set
power.set <- function(v)
{
  n <- length(v)  
  N <- 2^n - 1
  ps <- vector("list", N)
 
  for (i in 1:(N-1))
  {
    Nbin <- dec2bin(i)
    Nbin <- c(numeric(n-length(Nbin)), Nbin)
    Nbin <- rev(Nbin)
    ps[[i]] <- v[which(Nbin == 1)]
  }
 
  ps[[N]] <- v
 
  return(ps)
}
 
# dataset: variables in columns and observations as rows
# subset.min.size, subset.max.size: inclusive limits
# filename: if specified, the plot are saved as a png file with this filename
qqmultinorm <- function(dataset, subset.min.size = 1, subset.max.size = 4, filename = NULL)
{
  p <- ncol(dataset)
  n <- nrow(dataset)
 
  if (subset.min.size < 1) stop("subset.min.size < 1")
  if (subset.min.size > p) stop("subset.min.size > p")
  if (subset.max.size < 1) stop("subset.max.size < 1")
  if (subset.max.size > p) stop("subset.max.size > p")
  if (subset.min.size > subset.max.size) stop("subset.min.size > subset.max.size")
 
  if (is.null(colnames(dataset)))
    colnames(dataset) <- 1:p
 
  # We have p variables. If all is to be checked against each other,
  # then we have a power-set with 2^p subsets (including the empty set)
 
  # Here we get subset containing indexes of the variables to include
  # Note that power.set doesn't include the empty set.
  subsets <- power.set(1:p)
  subsets.len <- length(subsets)
 
  # To get the plots with the fewest variables first, we do a litte trick:
  # While we find out which plots to include, we build a list
  # where each element of a list is the index of the subset,
  # and the index of the element is the size of the subset.
  # (The +1 is because the limits are includesive!)
  s.included <- vector("list", subset.max.size - subset.min.size + 1)
 
  plots <- 0
 
  for (i in 1:subsets.len)
  {
    s <- subsets[[i]]
    s.len <- length(s)
 
    if (s.len >= subset.min.size && s.len <= subset.max.size)
    {
      plots <- plots + 1
      s.included[[s.len - subset.min.size + 1]] <- c(s.included[[s.len - subset.min.size + 1]], i)
    }
  }
 
  # Now it's possible to build the subset index vector; 
  # we disregard the size of each subset; no more need to know it.
  s.indexes <- c()
 
  for (s in s.included)
  {
    s.indexes <- c(s.indexes, s)
  }
 
  # We want a squared view
  plot.per.row <- ceiling(plots^(1/2))
  plot.per.column <- ceiling(plots^(1/2))
  plot.width <- 200
  plot.height <- 200
 
  if (!is.null(filename))
    png(file=paste(filename, ".png", sep=""), bg="white", width = plot.per.row * plot.width, height = plot.per.column * plot.height)
 
  par(mfrow = c(plot.per.row, plot.per.column))  
 
  # There's no need to calculate a whole lot several times:
  ybar <- as.vector(colMeans(dataset))
 
  S <- as.matrix(var(dataset))
 
  current <- 1  
  for (i in s.indexes)
  {
    s <- subsets[[i]]
    s.len <- length(s)
 
    if (s.len > subset.max.size)
      next
 
    cat("Processing subset no.", current, "out of", plots, "\n")
 
    # Container for our values
    squared.dist <- numeric(n)
 
    # qr.solve(A) = A^(-1)  
    Sinv <- qr.solve(S[s,s])
 
    # Then calculate the squared distance for each datapoint
    for (i in 1:n)
    {
      c <- dataset[i,s] - ybar[s]
      squared.dist[i] <- t(c) %*% Sinv %*% c
    }
 
    # Finding the order statistic
    squared.dist <- sort(squared.dist)
 
    qqchisq(squared.dist, paste(colnames(dataset)[s], collapse=", "), s.len)
 
    current <- current + 1
  }
 
  if (!is.null(filename))
    dev.off()
}
 
# Example:
A <- matrix(rnorm(2000, mean=3, sd=2), ncol=8)
qqmultinorm(A, 1, 3, "multinorm-1-3")
#qqmultinorm(A, 4, 4, "multinorm-4")
#qqmultinorm(A, 5, 5, "multinorm-5")
#qqmultinorm(A, 6, 8, "multinorm-6-8")